|
| Status |
Public on Feb 13, 2019 |
| Title |
MV4;11 untreated replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
MV4;11 cells were inoculated subcutaneously in the flank of NOD/SCID (NOD/SCID NOD.CB17-Prkdcscid/SzJ) mice.
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: Subcutaneous MV4;11 tumor
treatment: untreated
|
| Treatment protocol |
> 1 million MV4;11 cells were inoculated subcutaneously in the flank of NOD/SCID (NOD/SCID NOD.CB17-Prkdcscid/SzJ) mice. When tumors measured around 100 mm3, mice were treated with CBL0137 (70 mg/kg CBL0137 intravenously) on day 0 and day 8. Tumors were harvested 24h post last injection on day 8. Tumors were also harvested from untreated mice. Tumors were flash frozen in liquid nitrogen and RNA was isolated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Trizol
RNA-seq libraries were generated using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold prep kit using 1 μg of RNA input
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNA sequencing data of MV4;11 untreated replicate 2
MVcontr2
|
| Data processing |
Illumina paired-end RNA sequencing data was aligned using STAR to the human genome assembly hg19 and mouse genome assembly mm10
BAM files were sorted and index using SAMtools
Gene expression and isoform expression counts were calculated using RSEM
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: txt file contains the TPM counts for each gene in each of the samples
|
| |
|
| Submission date |
Feb 12, 2019 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Michelle Haber |
| E-mail(s) |
mhaber@ccia.org.au
|
| Organization name |
Children's Cancer Institute
|
| Street address |
Lowy Cancer Research Centre, PO BOX 81
|
| City |
Randwick |
| State/province |
NSW |
| ZIP/Postal code |
2031 |
| Country |
Australia |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE126442 |
Gene expression analysis of a subcutaneous MV4;11 tumor treated with curaxin CBL0137. |
|
| Relations |
| BioSample |
SAMN10920288 |
| SRA |
SRX5367838 |
